[gmx-users] Check for bad contacts and/or reduce the timestep

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:

<snip>

> Steepest Descents converged to machine precision in 34 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -3.7206969e+04
> Maximum force     =  2.0111207e+04 on atom 1217
> Norm of force     =  6.9283209e+02
> 
> I don't understand constraints I need to turn off, since I haven't 
> mentioned any in my grompp file.
> 

This is just generic advice that mdrun provides.  The fact is your starting 
structure contains atomic overlap or clashes that cannot be resolved by energy 
minimization.  Have a look at the trajectory and see if you can get some insight 
into where things are going wrong (since problematic atom numbers are being 
printed, and perhaps re-consider how you built your system.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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